The City of Phenix City applied for and received a National Pollutant Discharge Elimination System (NPDES) Phase II Stormwater Permit in March 2003. The original permit was issued for a 5-year time period ending in March 2008. The City of Phenix City sent the General Phase II MS4 Stormwater Permit Renewal Notice of Intent and the accompanying fee on August 31, 2007, for Permit Number ALR040019.

On February 17, 2009, the City of Phenix City sent an updated Notice of Intent to reflect changes in Responsible Official and Permit contact due to personnel changes in the positions of Mayor and City Engineer. The city continued to operate under this permit while the new NPDES permit was finalized. On October 29, 2009, after reviewing the first draft of the new permit, the City of Phenix City submitted comments to the ADEM Water Division. On September 23, 2010, a Phenix City representative attended the NPDES Construction General Permit Update in Auburn, Alabama. Having received the revised draft of the new MS4 permit on February 12, 2010, the City of Phenix City once more submitted comments to the ADEM Water Division. On January 31, 2011, the City of Phenix City received the reissued NPDES Permit No. ALR0400019, and is currently implementing all changes in this permit period.